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Visible crew/equipment: After Zhaan has taken control of the Halosian ship, when Zhaan's transmission appears on Moya's clamshell viewer, in the shots facing Rygel, John, and Aeryn (in each others' bodies) we can see the puppeteer, who's wearing a headset, with his right arm up in Rygel's sleeve. Fun to watch.
Chosen answer: It's never explained. John mentions a theory that his less technologically developed craft simply interferes with the wormhole less than the "superior" Vipers, but they never make a concrete determination on that point. But we also have to take into account the fact that Moya traverses wormholes with no ill effect as well.
Garlonuss ★